• Header of Geometric Morphometrics at Transmitting Science

Advanced Courses in Life Sciences

Registration closed

PLEASE NOTE:
Registration for this course is not yet available.
If you want to receive information once the registration is open, please subscribe without any obligation by selecting the topic Geometric Morphometrics.

6th Edition

3D Geometric Morphometrics

May 23rd-27th, 2016, Barcelona (Spain)

3D Geometric MorphometricsThis course is entitled to teach the main concepts of shape analysis based on three-dimensional landmark coordinates. In this course we you will learn to manipulate 3D models and use them to collect landmark data, take measurements, and to quantify and visualize the main differences in shape.

LOCATION

Centre de Restauració i Interpretació Paleontològica

C/ Mestre J. Lladós, nº 1
08781 Els Hostalets de Pierola, Barcelona.

Spain – CRIP

LANGUAGE

English

COURSE LENGHT & ECTS

35 hours on-site.

This course is equivalent to 3.5 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

PLACES

Places are limited to 20 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Instructor

Melissa Tallman instructor for Transmitting Science

Dr. Melissa Tallman
Grand Valley State University
United States of America

Coordinator

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Requirements

Graduate or postgraduate degree in Biomedical, Life or Earth Sciences, basic knowledge of statistics. No previous knowledge of Geometric Morphometrics is required.

All participants must bring their own personal laptop (Windows).

Program

Types of data acquisition.

Using a microscribe.
Collecting CT scans & Surface Scans.
– Demonstration of Stratovan Checkpoint.

Brief Review of Fundamentals of Morphometrics.
– How to choose landmarks.
– Generalized Procrustes Analysis.
– Other types of alignment.
– Thin plate spline warping.

Processing Microscribe data.
– Using DVLR to merge two views.
– Using resample to resample a line.

Using Landmark Editor to collect data on surfaces.
– Sliding semi-landmarks (using R geomorph package).

How to do a precision test on 3D data.

Data exploration: PCA analyses.
– Using Morphologika.
– Using MorphoJ.
– Between-group PCAs.
– PCAs in Procrustes form space.

Visualizing shape change.
– Using MorphoJ in conjunction with Landmark Editor.
– Making calculations and visualizing shape changes in PCA morphospace.
– Calculating PCA scores post hoc.

Data exploration: Regressions.
– Visualizing change that is associated with size (MorphoJ).
– Removing change associated from size from your data (MorphoJ).
– Common allometric trajectories.
– Comparing vector directions.
– Extracting linear dimensions from 3D data and using them as covariates.

Data exploration: PLS analyses.
– Using MorphoJ to mean center (or not).
– Visualizing shape change in Landmark editor.

Data exploration: Phylogeny.
– Visualizing shape changes in MorphoJ along a tree.
– Importing covariates and visualizing shape change associated with taxonomy (using MorphoJ).
– Creating a phyomorphospace.
– Correcting for phylogeny in PCA.

Data interpretations: Using mean configurations (PAST) and Procrustes distances.
– Minimum spanning trees.
– Variability within a sample (comparing fossil distributions to extant distributions).

Retrodeformation.


Programs that we will use:

Stratovan Checkpoint (temporal licences will be provided during the course).
– DVLR (free).
– Resample (free).
Landmark Editor (free).
Morphologika (free).
MorphoJ (free).
PAST (free).
R (free, only for sliding semilandmarks, no previous knowledge is required).
– Microsoft Excel.

Testimonials

You will find below some testimonials from former participants to previous editions of this course:

Jamie MacLaren

“Throughout the course, we dabbled in Landmark editor, Morphologika, MorphoJ, PAST, Meshlab, Checkpoint, … the list goes on. It can safely be said that much knowledge was gleaned from our excellent instructor, Dr. Melissa Tallman, and that no matter what organisms we are planning to study, we will now know how to apply the programs to answer our question…well, for the most part! All in all, the course was a roaring success in my eyes, and I hope for the rest of the participants also. Both Zebo and I would like to thank Sole, Lissa and Juanvi for their organization, their patience, their culinary expertise respectively…and, of course, their coffee. It has been a memorable trip, I have made many good contacts and hopefully some good friends, all of whom I hope to see on the academic circuit in the near future.” (4th Edition)

You can read more in his blog here.

Jamie MacLarenUniversity of Antwerp, Belgium

Previous editions of this course

5th Edition, May 4th-8th, 2015

Course 3D Geometric Morphometrics - 5th Edition, May 4th-8th, 2015Eight people belonging to the following countries and institutions participated in this edition:

  • Spain: Institut Català de Paleontologia Miquel Crusafont, University of Girona.
  • France: Muséum national d’Histoire naturelle.
  • Switzerland: University of Bern.
  • United Kingdom: University of Durham.
  • Finland: University of Helsinki.

4th Edition, May 20th-24th, 2014

Course 3D Geometric Morphometrics - 4th Edition, May 20th-24th, 2014Nineteen people belonging to the following countries and institutions participated in this edition:

  • United States of America: Appalachian State University, Texas A&M University, The University of New Mexico.
  • Spain: Centre for Genomic Regulation.
  • Greece: Hellenic Centre for Marine Research, National and Κapodistrian University of Athens.
  • The Netherlands: Leiden University, Naturalis Biodiversity Center.
  • Mexico: National Autonomous University of Mexico.
  • United Kingdom: Plymouth University.
  • Italy: Second University of Naples.
  • Germany: Senckenberg Gesellschaft für Naturforschung.
  • People’s Republic of China: The University of Hong Kong.
  • Belgium: University of Antwerp.
  • Switzerland: University of Zurich.

3rd Edition, May 15th-17th, 2013

Course 3D Geometric Morphometrics - 3rd Edition, May 15th-17th, 2013Fourteen people belonging to the following countries and institutions participated in this edition:

  • Slovenia: University of Maribor.
  • United States of America: Texas A&M University, Virginia Institute of Marine Science, University of Louisiana at Lafayette.
  • People’s Republic of China: Chinese Academy of Sciences.
  • The Netherlands: Leiden University.
  • Switzerland: University of Basel, University of Zurich.
  • Colombia: Universidad Nacional de Colombia.
  • Germany: Friedrich-Schiller-Universität Jena.
  • Italy: Università degli Studi di Milano.
  • Spain: Universitat de València.

2nd Edition, July 17th-20th, 2012

Course 3D Geometric Morphometrics - 2nd Edition, July 17th-20th, 2012Fourteen people belonging to the following countries and institutions participated in this edition:

  • United Kingdom: University College London.
  • Germany: Bayerische Staatssammlung für Paläontologie und Geologie, Ludwig Maximilians Universität Munich.
  • France: University of Poitiers.
  • Portugal: University of Coimbra.
  • United States of America: Texas A&M University, University of Pennsylvania.
  • Sweden: Uppsala University.
  • The Netherlands: Leiden University.
  • Spain: Universidad Complutense de Madrid, Institut Català de Paleontologia Miquel Crusafont, University of Barcelona.
  • Poland: Wroclaw University.

Fees

  • Course Fee
  • Early bird (until February 15th, 2016)
  • 440
  • Regular (after February 15th, 2016)
  • 615
  • This includes course material, coffee breaks and lunches.
  • Accommodation Package
  • Early bird (until February 15th, 2016)
  • 300
  • Regular (after February 15th, 2016)
  • 300
  • This includes local transportation, lodging, breakfasts, dinners and social (tourist) activities.
  • Course Fee + Accommodation Package
  • Early bird (until February 15th, 2016)
  • 740
  • Regular (after February 15th, 2016)
  • 915
  • This includes course material, coffee breaks and lunches.

We offer the possibility of paying in two instalments (contact the course coordinator). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

If you take the Accommodation Package you will be hosted in the Youth Hostel Can Roviralta, in shared dormitories (common bathrooms), although you will only share rooms with other classmates. The possibility exists that the dormitories will be mixed. Therefore, if this is an inconvenience for you, and you require staying in a dormitory with only women, or only men, please indicate so in the “Comments” field of the Registration form (see below).

A supplemental charge will be added if you prefer to stay in a single room with private bathroom. The number of rooms is limited and if you prefer to have a single room, let us know it as soon as possible. If you want more information on this please contact the course coordinator.

Please be aware that from the centre of Barcelona city it takes about one hour by car and one hour and a half by public transport to arrive to Els Hostalets de Pierola. Course participants will find that staying in Els Hostalets de Pierola is more convenient.

If you do not want the Accommodation Package, accommodation is available in places other than Els Hostalets de Pierola. You may stay in Barcelona city, Martorell or Igualada. You will find information about Hotels in Martorell here, and information about Hotels in Igualada here.

How to get to Els Hostalets de Pierola from Barcelona city, Martorell and Igualada.

Youth Hostel Can Roviralta (Els Hostalets de Pierola, Barcelona, Spain)

Funding

Former participants will have a 5 % discount on the Course Fee.

Unfortunately there are no scholarships available for this course. However a 20 % discount on the Course Fee is offered for members of some organizations (Organizations with discount). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Spanish unemployed scientists, as well as Spanish PhD students without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Schedule

Course ScheduleCourse + Accommodation Package Schedule
Sunday, May 22nd, 201619:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Els Hostalets de Pierola. If you are planning to arrive later, you can find more information in How to get there.
20:00 Registration in the Youth Hostel.
20:30 Dinner.
Monday, May 23rd through Friday, May 27th, 20169:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.

There will be two coffee breaks each day, halfway through each lesson session.

8:30 to 9:00 Breakfast.
9:30 to 13:30 Lessons.
13:30 to 15:00 Lunch.
15:00 to 18:00 Lessons.
20:30 Dinner.

There will be two coffee breaks each day, halfway through each lesson session.

Saturday, May 28th, 20168:30 to 9:00 Breakfast.
9:15 Meeting point in the Youth Hostel to take the bus to visit a wine cellar.
10:00 Arrival at the wine cellar.
11:30 Bus to Barcelona city.
13:00 Arrival at Plaza Catalunya (Barcelona).

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Organizers

Transmitting Science Logo
Centre de Restauració i Interpretació Paleontològica (CRIP) Logo
Institut Català de Paleontologia Miquel Crusafont (ICP) Logo

Collaborators

Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo
Distributed European School of Taxonomy (DEST) Logo
European Association of Vertebrate Palaeontologists (EAVP) Logo
Sociedade Brasileira de Paleontologia (SBP) Logo

Sponsor

Stratovan Logo
Registration closed

PLEASE NOTE:
Registration for this course is not yet available.
If you want to receive information once the registration is open, please subscribe without any obligation by selecting the topic Geometric Morphometrics.

© Copyright - Transmitting Science